ROME, Sept. 17 — Pope Benedict XVI sought Sunday to extinguish days of anger and protest among Muslims by issuing an extraordinary personal apology for having caused offense with a speech last week that cited a reference to Islam as “evil and inhuman.”

“I am deeply sorry for the reactions in some countries to a few passages of my address,” the pope told pilgrims at the summer papal palace of Castel Gandolfo, “which were considered offensive.’’

“These were in fact quotations from a medieval text, which do not in any way express my personal thought,” the pope, 79, said in Italian, according to the official English translation.

“The true meaning of my address,” he said, “in its totality was and is an invitation to frank and sincere dialogue, with great mutual respect.”

His statement came amid much worry in the church about violence and any erosion of the status of the pope as a neutral figure for peace among faiths. In Somalia on Sunday, the Italian Foreign Ministry reported, an Italian nun was shot to death, although it was unclear if this was related to the pope’s remarks. A day earlier, five churches were firebombed in the West Bank and one in Iraq.

Although Benedict’s predecessor, John Paul II, issued several apologies for the historical failings of the church, experts said it appeared to be the first time in recent memory that a pope had made such a direct statement of personal regret. “This is really, really abnormal,” said Alberto Melloni, professor of history at the University of Modena who has written several books on the Vatican. “It’s never happened as far as I know.”

Beyond the anger among Muslims, the pope’s comments have also provoked a complicated debate in Italy and among many Catholics, on issues including whether he appreciated the reaction he would provoke and whether the pope’s speeches, which he usually writes himself, are properly vetted by a Vatican undergoing a bureaucratic transition.

Several Vatican officials, who spoke on condition of anonymity because they were not authorized to discuss the issue publicly, said they had expressed concern before the speech was delivered that it might be negatively received by Muslims or be misconstrued by the news media as an attack on Islam.

And for many conservatives here, fearful of terrorist attacks in the name of Islam and rising Muslim immigration in Europe, the remarks of the pope — despite his own denial that he meant to criticize — amounted to a rare public airing of a delicate concern many of them share: whether, in fact, Islam is at the moment especially prone to violence.

Silvio Berlusconi, the former prime minister, said Saturday that the comments amounted to “an opening, a positive provocation, and so for this reason he is a great pope, with a great intelligence.”

The pope made his own public statement on Sunday after two other clarifications from senior Vatican officials since the speech was delivered last Tuesday at Regensburg University, in Germany, where the German-born pope used to teach theology. The speech was largely a scholarly address criticizing the West for submitting itself too much to reason, for walling belief in God out of science and philosophy. But he began by recounting a conversation on the truths of Christianity and Islam that took place between a 14th-century Byzantine Christian emperor, Manuel II Paleologus, and a Persian scholar.

“He said, I quote, ‘Show me just what Muhammad brought that was new, and there you will find things only evil and inhuman, such as his command to spread by the sword the faith he preached,’ ’’ the pope said.

He also briefly discussed the Islamic concept of jihad, which he defined as “holy war,” and said violence in the name of religion was contrary to God’s nature and to reason.

At the same time, without mentioning Islam specifically, he suggested reason as the basis for “that genuine dialogue of cultures and religions so urgently needed today.”

In the speech, he did not say whether he agreed with the quotations he cited about violence and Islam — but on Sunday he distanced himself strongly from them.

It was not immediately clear whether this would tamp down the anger, which recalled the furor earlier this year after European newspapers published cartoons unflattering to the Prophet Muhammad.

Photo

Hamas security guards protected a church in Gaza City, where a Catholic priest was meeting Sunday with a group of Palestinian Muslims.Credit
Abid Katib/Getty Images

In Egypt, a senior member of the Muslim Brotherhood, which had been critical of the pope, initially said Sunday that the pope’s remarks represented a “good step toward an apology.” Later comments from the group, however, seemed to cast doubt on whether it fully accepted the pope’s statement.

In Gaza, the Palestinian prime minister, Ismail Haniya, denounced attacks on some half-dozen churches there and in the West Bank. In Bethlehem, sacred to Christians as the birthplace of Jesus and home to many Arab Christians, police presence was higher than usual.

“The Christian brothers are a part of the Palestinian people, and I heard the highest Christian authority in Palestine denouncing the statements against Islam and against Muslims,” Mr. Haniya told reporters.

In Iran, several hundred theological students were given the day off to protest in Qum, the nation’s center for religious study, as the Vatican envoy in Tehran was summoned for an official complaint about the remarks. Several radical Iraqi groups posted threats on the Internet against the Vatican and Christians in general.

In Mogadishu, the capital of the former Italian colony of Somalia, the Italian nun died after being shot several times in an ambush in a hospital in which a Somali bodyguard was also killed. It was unclear if the attack was retribution for the pope’s remarks, though the Vatican issued a response.

The Rev. Federico Lombardi, the chief Vatican spokesman, was quoted by the ANSA news agency as calling the killing “horrible.” “We hope it remains an isolated incident,” he said.

While anger remained high in Turkey, the nation’s foreign minister, Abdullah Gul, said Sunday that he expected Benedict’s planned trip there in November would go ahead. But he called the pope’s remarks “really regrettable.”

The Vatican’s new secretary of state, Cardinal Tarcisio Bertone, also said on Sunday that he expected the pope’s visit to Turkey to proceed.

“For the time being, there is no reason why it should not,” he told the ANSA news agency.

The furor, which has left Benedict’s 17-month papacy with its first major crisis, has also set off a round of second-guessing in the Vatican and among church experts about exactly what happened.

First among the questions — which the pope denied Sunday — is whether he in fact intended to make a statement about Islam and violence. Second is whether he realized the extent of the reaction.

But more concretely, experts said, the issue raised questions both about how the church operates under this new pope, and to what extent his statements are checked and balanced diplomatically now that he is no longer an academic but leader of the world’s billion Roman Catholics.

Benedict is used to writing his own speeches, and several Vatican officials said he wrote Tuesday’s address, one of the most significant of the papacy, by himself. The officials said there was concern in the Vatican before he delivered it, both about the reaction among Muslims and how the news media would portray the passages relating to Islam.

That concern was relayed up the chain of command, the officials said, but it is not clear if it reached the pope.

At a time when the Vatican has just replaced its second-in-command and its foreign minister, many experts also said that did not have enough experts on Islam to gauge reaction to any papal statements.

“They have nobody to really ask,” said the Rev. Thomas Michel, secretary for inter-religious dialogue for the Jesuit order of priests. “Whoever looked at it and let that go through is someone who doesn’t understand Muslims at all.”

In February, Benedict reassigned the Vatican’s most senior Arabist, Archbishop Michael Fitzgerald, then the head of inter-religious dialogue, to Cairo as the Vatican envoy there. The move was seen at the time by some church experts as a sign of Benedict’s skepticism about the value of dialogue with Muslims.

“I think one may say, if it is not too impolite, that it is time to bring back Monsignor Fitzgerald,” said Mr. Melloni, the Vatican scholar.

A version of this article appears in print on , on Page A1 of the New York edition with the headline: In a Rare Step, Pope Expresses Personal Regret. Order Reprints|Today's Paper|Subscribe